This dataset provides results of a targeted bacterial community metagenomic analysis of surface water, groundwater, and sand samples at Jeorse Park on Lake Michigan in East Chicago, Indiana. Seventy-two samples were collected from 6 sites in 2017. Samples were analyzed for the 16S ribosomal RNA (16S rRNA) gene (the S in 16S refers to the rate of sedimentation, in Svedberg units, of the RNA molecule in a centrifugal field), and one sample was excluded because it produced too few reads. The 16S rRNA gene is the most conserved of three rRNA genes (16S, 23S, and 5S) and is considered the most reliable for identification and taxonomic classification of bacterial species (Bouchet and others, 2008). Taxonomic analysis was performed using Illumina paired-end sequencing by MiSeq to sequence V3-V4 of the gene. Determination of the relative abundance of bacterial species found in water can be used to track sources of fecal contamination by detecting host-specific markers in the sample.
The U.S. Geological Survey (USGS), in cooperation with the Great Lakes Restoration Initiative, collected data to study the sources and occurrences of continual high E. coli detections at urban beaches along the Lake Michigan shoreline in Northwest Indiana and northeastern Illinois. High E. coli detections cause the beaches to be closed for recreational use until results from additional samples verify that E. coli levels have fallen below the threshold of 235 cells per 100 ml. The project used microbial source tracking (MST) and metagenomics analyses to identify the sources of E. coli. Additionally, continuous water quality parameters and surface-water samples were collected to look at biological and environmental indicators. Synoptic surveys of water quality, circulation/transport, and bathymetry were done to help study surface-water flow patterns. Groundwater samples were taken to compare with surface-water E. coli results. Groundwater wells were installed at Jeorse Park Beach in 2017 and additional wells were installed at Whihala West beach in late 2017 and early 2018.
This data release contains three files. One file, entitled "metagenomics_sample_identification.txt,” contains a list of each sample, along with the site identifier (site ID), station name, replicate number, date of sampling, and substrate from which the sample was taken. The next file, entitled “metagenomics_taxonomy.txt,” contains a taxonomic classification of the 16S rRNA sequences obtained from every sample. The third file, contains metadata regarding the collection and analysis of the samples. Reference: Bouchet, Valerie, Huot, Heather, and Goldstein, Richard, 2008, Molecular genetic basis of ribotyping: Clinical Microbiology Reviews, 21(2), 262-273, https://doi.org/10.1128/cmr.00026-07.